# 导入环境
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/nas/health_data/anaconda3/envs/gnorm2/lib/
export PATH=$PATH:/mnt/nas/health_data/anaconda3/envs/gnorm2/bin/
cd /mnt/nas/health_data/chatllm/servers/GNorm2

INPUT=/mnt/nas/health_data/data/ftp.ncbi.nlm.nih.gov/pubmed/PubTator/$1
SR=/mnt/nas/health_data/data/ftp.ncbi.nlm.nih.gov/pubmed/PubTator_SR/$1
GNR=/mnt/nas/health_data/data/ftp.ncbi.nlm.nih.gov/pubmed/PubTator_GNR/$1

SA=/mnt/nas/health_data/data/ftp.ncbi.nlm.nih.gov/pubmed/PubTator_SA/$1
OUTPUT=/mnt/nas/health_data/data/ftp.ncbi.nlm.nih.gov/pubmed/PubTator_NER/$1

# SR
java -Xmx10G -Xms10G -jar GNormPlus.jar $INPUT $SR setup.SR.txt


# # GNR+SA (CUDA_VISIBLE_DEVICES=3 )
/mnt/nas/health_data/anaconda3/envs/gnorm2/bin/python GeneNER_SpeAss_run.py -i $SR -r $GNR -a $SA -n gnorm_trained_models/geneNER/GeneNER-Bioformer.h5 \
-s gnorm_trained_models/SpeAss/SpeAss-Bioformer.h5

# # GN
java -Xmx10G -Xms10G -jar GNormPlus.jar $SA ${OUTPUT} setup.GN.txt
